react-msaview 3.1.11 → 3.1.12

package/dist/launchInterProScan.js

@@ -1,6 +1,7 @@
+import { getSession } from '@jbrowse/core/util';
 import { jsonfetch, textfetch, timeout } from './fetchUtils';
 const base = `https://www.ebi.ac.uk/Tools/services/rest`;
-async function runInterProScan({ seq, onProgress, onJobId, programs, }) {
+async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
     const jobId = await textfetch(`${base}/iprscan5/run`, {
         method: 'POST',
         body: new URLSearchParams({
@@ -9,39 +10,75 @@ async function runInterProScan({ seq, onProgress, onJobId, programs, }) {
             programs: programs.join(','),
         }),
     });
-    onJobId(jobId);
+    onJobId?.(jobId);
     await wait({
         jobId,
         onProgress,
     });
-    return loadInterProScanResults(jobId);
+    return loadInterProScanResultsWithStatus({ jobId, model });
 }
-export async function loadInterProScanResults(jobId) {
-    return (await jsonfetch(`${base}/iprscan5/result/${jobId}/json`));
+export function loadInterProScanResults(jobId) {
+    return jsonfetch(`${base}/iprscan5/result/${jobId}/json`);
 }
 async function wait({ onProgress, jobId, }) {
     const url = `${base}/iprscan5/status/${jobId}`;
-    // eslint-disable-next-line no-constant-condition
-    while (true) {
-        for (let i = 0; i < 10; i++) {
-            await timeout(1000);
-            onProgress({ msg: `Checking status... ${10 - i}`, url });
-        }
-        const result = await textfetch(url);
-        if (result === 'FINISHED') {
-            break;
+    try {
+        // eslint-disable-next-line no-constant-condition
+        while (true) {
+            for (let i = 0; i < 10; i++) {
+                await timeout(1000);
+                onProgress({ msg: `Checking status ${10 - i}`, url });
+            }
+            const result = await textfetch(url);
+            if (result.includes('FINISHED')) {
+                break;
+            }
         }
     }
+    finally {
+        onProgress();
+    }
 }
-export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, }) {
-    onProgress({ msg: `Launching ${algorithm} MSA...` });
-    if (algorithm === 'interproscan') {
-        const result = await runInterProScan({ seq, onJobId, onProgress, programs });
+export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, }) {
+    try {
+        onProgress({ msg: `Launching ${algorithm} MSA` });
+        if (algorithm === 'interproscan') {
+            const result = await runInterProScan({
+                seq,
+                onJobId,
+                onProgress,
+                programs,
+                model,
+            });
+            return result;
+        }
+        else {
+            throw new Error('unknown algorithm');
+        }
+    }
+    finally {
         onProgress();
-        return result;
     }
-    else {
-        throw new Error('unknown algorithm');
+}
+export async function loadInterProScanResultsWithStatus({ jobId, model, }) {
+    try {
+        model.setStatus({
+            msg: 'Downloading results of ' +
+                jobId +
+                ' (for larger sequences this can be slow, click status to download and upload in the manual tab)',
+            url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
+        });
+        const ret = await loadInterProScanResults(jobId);
+        model.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
+        model.setShowDomains(true);
+        getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
+    }
+    catch (e) {
+        console.error(e);
+        getSession(model).notifyError(`${e}`, e);
+    }
+    finally {
+        model.setStatus();
     }
 }
 //# sourceMappingURL=launchInterProScan.js.map

package/dist/launchInterProScan.js.map

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package/dist/model.d.ts

@@ -49,7 +49,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    featureMode: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("mobx-state-tree").ISimpleType<"MsaView">;
     height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -58,17 +58,13 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
     colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
     treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree" /**
-         * #property
-         */).ISimpleType<"UriLocation">;
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import(
-        /**
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree" /**
          * #volatile
-         */
-        "mobx-state-tree").IModelType<{
+         */).IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -105,14 +101,15 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         locationType: "UriLocation";
         uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        locationType: import("mobx-state-tree" /**
+         * #action
+         * set mouse position (row, column) in the MSA
+         */).ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            internetAccountType: import("mobx-state-tree" /**
-             * #action
-             */).ISimpleType<string>;
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -336,13 +333,6 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      *
      */
     loadedInterProAnnotations: undefined | Record<string, InterProScanResults>;
-    /**
-     * #volatile
-     */
-    interProScanJobIds: {
-        jobId: string;
-        date: number;
-    }[];
 } & {
     /**
      * #action
@@ -374,7 +364,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setFeatureMode(arg: boolean): void;
+    setShowDomains(arg: boolean): void;
     /**
      * #action
      */
@@ -615,10 +605,6 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     toggleTrack(id: string): void;
-    /**
-     * #action
-     */
-    addInterProScanJobId(arg: string): void;
     /**
      * #action
      */
@@ -713,14 +699,6 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         [k: string]: string;
     };
 } & {
-    /**
-     * #action
-     */
-    loadInterProScanResults(jobId: string): Promise<void>;
-    /**
-     * #action
-     */
-    queryInterProScan(programs: string[]): Promise<void>;
     /**
      * #action
      */
@@ -760,7 +738,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     bgColor: boolean;
     colorSchemeName: string;
     id: string;
-    featureMode: boolean;
+    showDomains: boolean;
     subFeatureRows: boolean;
     rowHeight: number;
     scrollY: number;

package/dist/model.js

@@ -7,7 +7,7 @@ import { saveAs } from 'file-saver';
 // jbrowse
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
 import { openLocation } from '@jbrowse/core/util/io';
-import { groupBy, localStorageGetItem, localStorageSetItem, notEmpty, sum, } from '@jbrowse/core/util';
+import { groupBy, notEmpty, sum, } from '@jbrowse/core/util';
 // locals
 import { clamp, collapse, generateNodeIds, maxLength, setBrLength, skipBlanks, len, } from './util';
 import { colord } from 'colord';
@@ -28,7 +28,6 @@ import { DataModelF } from './model/DataModel';
 import { DialogQueueSessionMixin } from './model/DialogQueue';
 import { TreeF } from './model/treeModel';
 import { MSAModelF } from './model/msaModel';
-import { launchInterProScan, loadInterProScanResults, } from './launchInterProScan';
 /**
  * #stateModel MsaView
  * extends
@@ -47,7 +46,7 @@ function stateModelFactory() {
         /**
          * #property
          */
-        featureMode: false,
+        showDomains: false,
         /**
          * #property
          */
@@ -211,10 +210,6 @@ function stateModelFactory() {
          *
          */
         loadedInterProAnnotations: undefined,
-        /**
-         * #volatile
-         */
-        interProScanJobIds: JSON.parse(localStorageGetItem('msaview-interproscanqueries') || '[]'),
     }))
         .actions(self => ({
         /**
@@ -260,8 +255,8 @@ function stateModelFactory() {
         /**
          * #action
          */
-        setFeatureMode(arg) {
-            self.featureMode = arg;
+        setShowDomains(arg) {
+            self.showDomains = arg;
         },
         /**
          * #action
@@ -716,15 +711,6 @@ function stateModelFactory() {
                 self.turnedOffTracks.set(id, true);
             }
         },
-        /**
-         * #action
-         */
-        addInterProScanJobId(arg) {
-            self.interProScanJobIds = [
-                ...self.interProScanJobIds,
-                { jobId: arg, date: +Date.now() },
-            ];
-        },
         /**
          * #action
          */
@@ -923,34 +909,6 @@ function stateModelFactory() {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
-        async loadInterProScanResults(jobId) {
-            self.setStatus({ msg: 'Loading ' + jobId });
-            const ret = await loadInterProScanResults(jobId);
-            self.setStatus();
-            self.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
-        },
-        /**
-         * #action
-         */
-        async queryInterProScan(programs) {
-            const { rows } = self;
-            if (rows.length > 140) {
-                throw new Error('Too many sequences, please run InterProScan offline');
-            }
-            const ret = await launchInterProScan({
-                algorithm: 'interproscan',
-                programs: programs,
-                seq: rows
-                    .map(row => `>${row[0]}\n${row[1].replaceAll('-', '')}`)
-                    .join('\n'),
-                onProgress: arg => self.setStatus(arg),
-                onJobId: jobId => self.addInterProScanJobId(jobId),
-            });
-            self.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
-        },
         /**
          * #action
          */
@@ -1001,22 +959,6 @@ function stateModelFactory() {
                     this.initFilter(key);
                 }
             }));
-            addDisposer(self, autorun(async () => {
-                // const res = Object.fromEntries(
-                //   await Promise.all(
-                //     self.annotationTracks.map(async f => {
-                //       const d = await jsonfetch(
-                //         `https://jbrowse.org/demos/interproscan/json/${encodeURIComponent(f)}`,
-                //       )
-                //       return [
-                //         decodeURIComponent(f).replace('.json', ''),
-                //         d.result.results[0],
-                //       ] as const
-                //     }),
-                //   ),
-                // )
-                // self.setLoadedInterProAnnotations(res)
-            }));
             // autorun opens treeFilehandle
             addDisposer(self, autorun(async () => {
                 const { treeFilehandle } = self;
@@ -1081,9 +1023,6 @@ function stateModelFactory() {
                     self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 10 - self.marginLeft));
                 }
             }));
-            addDisposer(self, autorun(() => {
-                localStorageSetItem('msaview-interproscanqueries', JSON.stringify(self.interProScanJobIds));
-            }));
         },
     }))
         .postProcessSnapshot(result => {

package/dist/model.js.map

@@ -1 +1 @@
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package/dist/renderToSvg.js

@@ -44,29 +44,6 @@ async function render({ width, height, offsetX, offsetY, theme, model, includeMi
         React.createElement(Wrapper, { model: model },
             React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, height: height }))), createRoot);
 }
-// function renderMultiline({ model }: { model: MsaViewModel }) {
-//   const { treeAreaWidth, height } = model
-//   const clipId = 'tree'
-//   return (
-//     <Wrapper model={model}>
-//       <defs>
-//         <clipPath id={clipId}>
-//           <rect x={0} y={0} width={treeAreaWidth} height={height} />
-//         </clipPath>
-//       </defs>
-//       <g
-//         clipPath={`url(#${clipId})`}
-//         /* eslint-disable-next-line react/no-danger */
-//         dangerouslySetInnerHTML={{ __html: ctx1.getSvg().innerHTML }}
-//       />
-//       <g
-//         transform={`translate(${treeAreaWidth} 0)`}
-//         /* eslint-disable-next-line react/no-danger */
-//         dangerouslySetInnerHTML={{ __html: ctx2.getSvg().innerHTML }}
-//       />
-//     </Wrapper>
-//   )
-// }
 function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context, }) {
     const clipId1 = 'tree';
     const clipId2 = 'msa';

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.1.11";
+export declare const version = "3.1.12";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.11';
+export const version = '3.1.12';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.11",
+  "version": "3.1.12",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",

package/src/components/SequenceTextArea.tsx

@@ -22,8 +22,11 @@ export default function SequenceTextArea({ str }: { str: [string, string][] }) {
   const { classes } = useStyles()
   const [copied, setCopied] = useState(false)
   const [showGaps, setShowGaps] = useState(false)
+  const [showEmpty, setShowEmpty] = useState(false)
 
   const disp = str
+    .map(([s1, s2]) => [s1, showGaps ? s2 : s2.replaceAll('-', '')])
+    .filter(f => (showEmpty ? true : !!f[1]))
     .map(([s1, s2]) => `>${s1}\n${showGaps ? s2 : s2.replaceAll('-', '')}`)
     .join('\n')
   return (
@@ -44,6 +47,11 @@ export default function SequenceTextArea({ str }: { str: [string, string][] }) {
         checked={showGaps}
         onChange={() => setShowGaps(!showGaps)}
       />
+      <Checkbox2
+        label="Show empty"
+        checked={showEmpty}
+        onChange={() => setShowEmpty(!showEmpty)}
+      />
       <TextField
         variant="outlined"
         multiline

package/src/components/dialogs/DomainDialog.tsx

@@ -0,0 +1,38 @@
+import React, { useState } from 'react'
+import { Dialog } from '@jbrowse/core/ui'
+import { Tab, Tabs } from '@mui/material'
+
+// locals
+import InterProScanPanel from './InterProScanPanel'
+import UserProvidedResultPanel from './UserProvidedResultPanel'
+import TabPanel from './TabPanel'
+import { MsaViewModel } from '../../model'
+
+export default function LaunchDomainViewDialog({
+  handleClose,
+  model,
+}: {
+  handleClose: () => void
+  model: MsaViewModel
+}) {
+  const [choice, setChoice] = useState(0)
+  return (
+    <Dialog
+      maxWidth="xl"
+      title="Launch protein view"
+      onClose={() => handleClose()}
+      open
+    >
+      <Tabs value={choice} onChange={(_, val) => setChoice(val)}>
+        <Tab value={0} label="Automatic lookup" />
+        <Tab value={1} label="Manual" />
+      </Tabs>
+      <TabPanel value={choice} index={0}>
+        <InterProScanPanel model={model} handleClose={handleClose} />
+      </TabPanel>
+      <TabPanel value={choice} index={1}>
+        <UserProvidedResultPanel model={model} handleClose={handleClose} />
+      </TabPanel>
+    </Dialog>
+  )
+}